Updated To 3.3 And Now Having Issues With Permalink Structure

I just updated to the new 3.3 today and now I’m having a problem with my post now coming up properly formatted. In fact it’s all coming up as one big page instead of the post being separate the way they were prior to this update. They also seemed to have merged with my pages too. I have no clue what’s happening!

I am using prettylink pro on my site and was told to check the permalink structure on my site but I see that it is no longer me add a custom structure and every time that I attempt to save it as such, it revets back to “post name”.

Because of this issue the front page of my blog now looks distorted. I have disabled all of the plug ins and the issue still has not been resolved.